大庆地区犊牛肠道病毒种群的宏基因组学分析

doi:10.16431/j.cnki.1671-7236.2024.12.005

Abstract

Abstract: 【Objective】 The experiment was aimed to comprehend the composition and genetic variability of calf intestinal viruses within the dairy cattle population in the Daqing region,and furnish a theoretical framework for the detection of viral pathogens responsible for diarrhea in local calves.【Method】 A total of 155 fecal samples of calves were collected from dairy farms surrounding Daqing,which were divided into six diarrhea sample pools and three clinically asymptomatic sample pools.Total nucleic acid was extracted,high-throughput sequencing was performed based on Illumina sequencing platform,SPAdes and SOAPdenovo were used for sequence splicing and assembly,and viral population composition and genetic variation were analyzed according to the obtained sequences.【Result】 A total of 6 517 147 viral-related sequences from 21 viral families were successfully annotated.In the calf intestinal viral community,except for bacteriophaes,Coronaviridae exhibited the highest abundance,followed by Picornaviridae.Comparison of annotation results of the diarrhea samples with asymptomatic samples,the diversity of the virus population in the asymptomatic samples was significantly higher than that in the diarrhea samples,and it was found that the relative abundance of Parvoviridae, Picornaviridae and Reoviridae was higher in the diarrhea group samples compared to the non-diarrhea group.This study annotated multiple novel sequences of calf diarrhea viruses such as Bovine torovirus (BToV),Bovine kobuvirus (BKV) and Bovine norovirus (BNoV).In addition,for the first time,Bovine nebovirus was identified in calf feces in Heilongjiang region.Genetic evolution analysis on the assembled genomes of BRV,BCoV and BoAstV was conducted,and it showed that the predominant genotypes of BRV were identified as G6,G10,P[5] and P[11].The assembled full-length genome of BCoV showed the closest phylogenetic relationship with Coronavirus/Bo/BCoV6/2021/CHN,a prevalent strain in China.BoAstV sequences clustered consistently within the branch of enteric tissue tropism strains.【Conclusion】 The abundance of Coronaviraceae was the highest in the calf enterovirus population in Daqing area.The abundance of viral population in the diarrhea group samples was lower than that in the non-diarrhea group samples.Several calf diarrhea viruses,such as BToV,BKV and BNoV were annotated in the fecal samples.Additionally,BNeV was first annotated in calf feces from Heilongjiang province.Genetic evolution characteristics of local prevalent viruses such as BRV,BCoV and BoAstV were analyzed.These findings provided a theoretical basis for the detection of viral pathogens causing diarrhea in local calves.

Key words: calf intestinal virus; viral metagenomics; high-throughput sequencing

CLC Number:

S852.65⁺3

CHEN Tianjie, LI Yuduo, ZHOU Hualiang, ZHAO Huijun, ZHAO Jianjun. Metagenomic Analysis of Calf Intestinal Viral Population in Daqing Region[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(12): 5162-5173.

References

[1] LORENZ I, HUBER R, TREFZ F M.A high plane of nutrition is associated with a lower risk for neonatal calf diarrhea on Bavarian dairy farms[J].Animals, 2021, 11(11):3251-3261.
[2] DALL AGNOL A M, LORENZETTI E, LEME R A, et al.Severe outbreak of bovine neonatal diarrhea in a dairy calf rearing unit with multifactorial etiology[J].Brazilian Journal of Microbiology, 2021, 52(4):2547-2553.
[3] CHO Y I, YOON K J.An overview of calf diarrhea-Infectious etiology, diagnosis, and intervention[J].Journal of Veterinary Science, 2014, 15(1):1-17.
[4] SCHUSTER S C.Next-generation sequencing transforms today’s biology[J]. Nature Methods, 2008, 5(1):16-18.
[5] EDWARDS R A, ROHWER F.Viral metagenomics[J]. Nature Reviews Microbiology, 2005, 3(6):504-510.
[6] PAEZ-ESPINO D, ELOE-FADROSH E A, PAVLOPOULOS G A, et al.Uncovering earth’s virome[J].Nature, 2016，536(7617):425-430.
[7] CHEN X, ZHANG B, YUE H, et al.A novel Astrovirus species in the gut of yaks with diarrhoea in the Qinghai-Tibetan plateau, 2013[J].The Journal of General Virology, 2015, 96(12):3672-3680.
[8] NG T F, KONDOV N O, DENG X, et al.A metagenomics and case-control study to identify viruses associated with bovine respiratory disease[J].Journal of Virology, 2015, 89(10):5340-5349.
[9] LI Y, CHANG J, WANG Q, et al.Isolation of two Chinese Bovine enteroviruses and sequence analysis of their complete genomes[J].Archives of Virology, 2012, 157(12):2369-2375.
[10] GU W, MILLER S, CHIU C Y.Clinicalmetagenomic next-generation sequencing for pathogen detection[J].Annual Review of Pathology, 2019, 24(14):319-338.
[11] CHO Y I, HAN J I, WANG C, et al.Case-control study of microbiological etiology associated with calf diarrhea[J].Veterinary Microbiology, 2013, 166(3-4):375-385.
[12] 赵润涛.内蒙古犊牛粪样宏病毒组学研究及BKoV、BNeV荧光定量RT-PCR检测方法的建立[D].呼和浩特:内蒙古大学, 2022.ZHAO R T.Metagenomic study of bovine fecal samples in Inner Mongolia and establishment of fluorescent quantitative RT-PCR detection methods for BKoV and BNeV[D].Hohhot:Inner Mongolia University, 2022.(in Chinese)
[13] 付寅.天鹅及肉犊牛肠道微生物宏基因组学分析[D].郑州:河南农业大学, 2022.FU Y.Metagenomic analysis of intestinal microbiota in swans and veal calves[D].Zhengzhou:Henan Agricultural University, 2022.(in Chinese)
[14] 陈伟.新生仔猪肠道细菌溯源及其与病毒组互作[D].广州：华南农业大学, 2019.CHEN W.Tracing of gut bacteria in newborn piglets and their interaction with viral groups[D].Guangzhou:South China Agricultural University, 2019.(in Chinese)
[15] ANDERSSON A F, BANFIELD J F.Virus population dynamics and acquired virus resistance in natural microbial communities[J].Science, 2008, 320(5879):1047-1050.
[16] LU X, HUA X, WANG Y, et al.Comparison of gut viral communities in diarrhoea and healthy dairy calves[J]. Journal of General Virology, 2021, 102(10):Doi:10.1099/jgv.0.001663.
[17] 王牧川, 岳华, 汤承, 等.重庆肉牛腹泻相关病毒的检测及遗传进化分析[J].中国畜牧兽医, 2017, 44(9):2731-2738.WANG M C, YUE H, TANG C, et al.Detection and genetic evolution analysis of diarrhea-related viruses in Chongqing beef cattle[J].China Animal Husbandry & Veterinary Medicine, 2017, 44(9):2731-2738.(in Chinese)
[18] 常丽云, 刘志勇, 李华伟, 等.唐山地区奶犊牛主要腹泻相关病原的流行病学调查[J].中国畜牧兽医, 2023, 50(7):2854-2864.CHANG L Y, LIU Z Y, LI H W, et al.Epidemiological investigation of major diarrhea-related pathogens in dairy calves in Tangshan area[J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(7):2854-2864.(in Chinese)
[19] GUO Z, HE Q, YUE H, et al.First detection of Nebovirus and Norovirus from cattle in China[J].Archives of Virology, 2018, 163(2):475-478.
[20] 李斯熠.我国部分省区牛纽布病毒的检测及其分子特征[D].成都:西南民族大学, 2022.LI S Y.Detection and molecular characteristics of Bovine norovirus in some provinces of China[D].Chengdu:Southwest Minzu University, 2022.(in Chinese)
[21] YAMASHITA T, ITO M, KABASHIMA Y, et al.Isolation and characterization of a new species of Kobuvirus associated with cattle[J].Journal of General Virology, 2003, 84(Pt 11):3069-3077.
[22] LILI H, CHAO X C, KEITH B, et al.Bovine kobuvirus-A comprehensive review[J].Transboundary and Emerging Diseases, 2021, 68(4):1886-1894.
[23] HOET A E, SMILEY J, THOMAS C, et al.Association of enteric shedding of Bovine torovirus (Breda virus) and other enteropathogens with diarrhea in veal calves[J].American Journal of Veterinary Research, 2003, 64(4):485-490.
[24] SHI Z, WANG W, CHEN C, et al.First report and genetic characterization of Bovine torovirus in diarrhoeic calves in China[J]. BMC Veterinary Research, 2020, 16(1):272.
[25] VAN DER POEL W H, VAN DER HEIDE R, VERSCHOOR F, et al.Epidemiology of Norwalk-like virus infections in cattle in the Netherlands[J].Veterinary Microbiology, 2003, 92(4):297-309.
[26] DI MARTINO B, DI PROFIO F, DI FELICE E, et al.Genetic heterogeneity of Bovine noroviruses in Italy[J]. Archives of Virology, 2014, 159(10):2717-2722.
[27] MENG W, CHEN Z, JIANG Q, et al.A multiplex Real-time fluorescence-based quantitative PCR assay for calf diarrhea viruses[J].Frontiers in Microbiology, 2024, 14:1327291.

Metagenomic Analysis of Calf Intestinal Viral Population in Daqing Region

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	SONG Peijia, JIN Yipeng, LIN Degui, LIN Jiahao. Clinical Research Progress on Canine Periodontal Diseases [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 838-845.
[2]	CHEN Yanxi, WANG Chen, LUO Yuan, ZHOU Yuancheng, XU Zhiwen, PENG Yuanyi, SONG Zhenhui, LIU Xiao. circRNA Expression Profile Analysis of PK-15 Cells Response to Seneca Virus A Infection [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 280-289.
[3]	GUO Luanying, LI Jialei, JIN Qinqin, MA Jun, LIU Quan. Research Progress on Bovine Hepacivirus [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(5): 1994-2000.
[4]	ZHAO Jibo, TAN Lei, PAN Hongbin, HUANG Chang, LIU Yong, WANG Guangzheng, DOU Tengfei, WANG Kun, LI Zijian, GE Changrong. Mining Molecular Genetic Markers Based on High-throughput Sequencing Technology and Its Accurate Application in Laying Hens Production [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(10): 3866-3878.
[5]	LI Wenjing, WEI Kaimin, ZHANG Shaoqiu, CHEN Yong. Effects of Walnut Green Husk and Its Extract on Intestinal Morphology,Mucosal Antioxidant Activity and Microbial Diversity of Yellow-feather Broilers [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(6): 2056-2065.
[6]	LI Pei, LIU Guomei, LIU Yingying, LIU Mandi, LI Yan, FAN Jinghui. Analysis of lncRNA Expression Profile in Porcine Intestinal Epithelial Cells Infected with Enterotoxigenic Escherichia coli F41 at Early Stage [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(5): 1707-1716.
[7]	WANG Anping, HAO Fuxing, ZHANG Shuo, XIE Jun, LIU Li, ZHU Shanyuan. Identification of Pathogen of Gosling Gout Using Viral Metagenomics [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(12): 4661-4670.
[8]	ZENG Maoqin, LIU Yanhan, ZHANG Qiandong, BI Wenwen, YE Ni, WANG Yizhou, YANG Ying, CHENG Zhentao, WEN Ming. Differential Analysis of miRNA Expression Profiles in Liver of Duck Infected with Duck Enteritis Virus [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(11): 4170-4181.
[9]	ZHANG Zijing, ZHU Xiaoting, LYU Shijie, JIN Lei, XU Jiawei, HUANG Yongzhen, LI Zhiming, WANG Xianwei, YU Xiang, YANG Shang, LI Jing, WANG Eryao, XU Zhaoxue, SHI Qiaoting. Study on the Structure and Function of Fecal Microbiome Between Diarrhea and Healthy Calves [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(9): 2779-2788.
[10]	ZHANG Mingyang, ZENG Maoqin, LIU Yanhan, ZHANG Piao, YANG Xia, YANG Ying, WEN Guilan, CHENG Zhentao, JIANG Haibo, WEN Ming. Transcriptome Analysis of Hybrid Sturgeons Intestinal Infected with Plesiomonas shigelloides [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(9): 2732-2740.
[11]	LIANG Xiaorui, WANG Danyang, QIAO Yanjie, ZHANG Baojun, SUN Guojie, SHAO Yongbin, GU Xinli, LUO Yan. Effects of Water Extract of Three Qingre Chinese Medicine on Intestinal Flora and Mucosal Barrier Function of Broilers [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(7): 2043-2054.
[12]	WANG Yunzhou, CHEN Fengmei, ZHANG Wanming, GUO Jianqiang, MA Chaoyin, HU Shilin. High Throughput Sequencing Analyzed Changes in the Yak Rumen Microflora after Qinghai Yaks Introduced to Shandong [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(7): 2013-2024.
[13]	JU Yan, LIU Huamiao, HE Jinming, WANG Lei, ZHAO Pei, ZHANG Ranran, DONG Yimeng, DONG Shiwu, TANG Lixin, XING Xiumei. Transcriptome Analysis of Antler in Aoluguya Reindeer Based on High-throughput Sequencing Technology [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(7): 1981-1989.
[14]	CHANG Weihua, WANG Juanhong, CUI Zilong. Construction of miRNA Library and Bioinformatics Analysis About Fetal Fibroblasts of Saanen Dairy Goat [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(11): 3436-3444.
[15]	LI Jiajia, SONG Jianling. Identification and Complete Genomic Analysis of a Newcastle Disease Virus from a Laying Hen [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(1): 221-228.